Genome-wide association study between CNVs and milk production traits in Valle del Belice sheep

被引:39
作者
Di Gerlando, Rosalia [1 ]
Sutera, Anna Maria [1 ]
Mastrangelo, Salvatore [1 ]
Tolone, Marco [1 ]
Portolano, Baldassare [1 ]
Sottile, Gianluca [2 ]
Bagnato, Alessandro [3 ]
Strillacci, Maria Giuseppina [3 ]
Sardina, Maria Teresa [1 ]
机构
[1] Univ Palermo, Dipartimento Sci Agr Alimentari & Forestali, Palermo, Italy
[2] Univ Palermo, Dipartimento Sci Econ Aziendali & Stat, Palermo, Italy
[3] Univ Milan, Dipartimento Med Vet, Milan, Italy
来源
PLOS ONE | 2019年 / 14卷 / 04期
关键词
COPY NUMBER VARIATION; CANDIDATE GENES; VARIANTS; RECEPTORS; PHENOTYPE; BREEDS; DNA;
D O I
10.1371/journal.pone.0215204
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Copy number variation (CNV) is a major source of genomic structural variation. The aim of this study was to detect genomic CNV regions (CNVR) in Valle del Belice dairy sheep population and to identify those affecting milk production traits. The GO analysis identified possible candidate genes and pathways related to the selected traits. We identified CNVs in 416 individuals genotyped using the Illumina OvineSNP50 BeadChip array. The CNV association using a correlation-trend test model was examined with the Golden Helix SVS 8.7.0 tool. Significant CNVs were detected when their adjusted p-value was <0.01 after false discovery rate (FDR) correction. We identified 7,208 CNVs, which gave 365 CNVRs after aggregating overlapping CNVs. Thirty-one CNVRs were significantly associated with one or more traits included in the analysis. All CNVRs, except those on OAR19, overlapped with quantitative trait loci (QTL), even if they were not directly related to the traits of interest. A total of 222 genes were annotated within the significantly associated CNVRs, most of which played important roles in biological processes related to milk production and health-related traits. Identification of the genes in the CNVRs associated with the studied traits will provide the basis for further investigation of their role in the metabolic pathways related to milk production and health traits.
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页数:13
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共 56 条
  • [1] Complex haplotypes, copy number polymorphisms and coding variation in two recently divergent mouse strains
    Adams, DJ
    Dermitzakis, ET
    Cox, T
    Smith, J
    Davies, R
    Banerjee, R
    Bonfield, J
    Mullikin, JC
    Chung, YJ
    Rogers, J
    Bradley, A
    [J]. NATURE GENETICS, 2005, 37 (05) : 532 - 536
  • [2] AN OPTIMUM TRANSFORMATION FOR SOMATIC-CELL CONCENTRATION IN MILK
    ALI, AKA
    SHOOK, GE
    [J]. JOURNAL OF DAIRY SCIENCE, 1980, 63 (03) : 487 - 490
  • [3] Identification of copy number variations and common deletion polymorphisms in cattle
    Bae, Joon Seol
    Cheong, Hyun Sub
    Kim, Lyoung Hyo
    NamGung, Suk
    Park, Tae Joon
    Chun, Ji-Yong
    Kim, Jason Yongha
    Pasaje, Charisse Flerida A.
    Lee, Jin Sol
    Shin, Hyoung Doo
    [J]. BMC GENOMICS, 2010, 11
  • [4] Underlying functional genomics of fat deposition in adipose tissue
    Bakhtiarizadeh, Mohammad Reza
    Moradi-Shahrbabak, Mohammad
    Ebrahimie, Esmaeil
    [J]. GENE, 2013, 521 (01) : 122 - 128
  • [5] Associated effects of copy number variants on economically important traits in Spanish Holstein dairy cattle
    Ben Sassi, Neila
    Gonzalez-Recio, Oscar
    de Paz-del Rio, Raquel
    Rodriguez-Ramilo, Silvia T.
    Fernandez, Ana I.
    [J]. JOURNAL OF DAIRY SCIENCE, 2016, 99 (08) : 6371 - 6380
  • [6] Transcriptome Analysis of Three Sheep Intestinal Regions reveals Key Pathways and Hub Regulatory Genes of Large Intestinal Lipid Metabolism
    Chao, Tianle
    Wang, Guizhi
    Ji, Zhibin
    Liu, Zhaohua
    Hou, Lei
    Wang, Jin
    Wang, Jianmin
    [J]. SCIENTIFIC REPORTS, 2017, 7
  • [7] Copy number variations and genome-wide associations reveal putative genes and metabolic pathways involved with the feed conversion ratio in beef cattle
    de Almeida Santana, Miguel Henrique
    Oliveira Junior, Gerson Antonio
    Mello Cesar, Aline Silva
    Freua, Mateus Castelani
    Gomes, Rodrigo da Costa
    da Luz e Silva, Saulo
    Leme, Paulo Roberto
    Fukumasu, Heidge
    Carvalho, Minos Esperandio
    Ventura, Ricardo Vieira
    Coutinho, Luiz Lehmann
    Kadarmideen, Haja N.
    Sterman Ferraz, Jose Bento
    [J]. JOURNAL OF APPLIED GENETICS, 2016, 57 (04) : 495 - 504
  • [8] Genome-wide detection of copy-number variations in local cattle breeds
    Di Gerlando, Rosalia
    Sardina, Maria Teresa
    Tolone, Marco
    Sutera, Anna Maria
    Mastrangelo, Salvatore
    Portolano, Baldassare
    [J]. ANIMAL PRODUCTION SCIENCE, 2019, 59 (05) : 815 - 822
  • [9] Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms
    Diskin, Sharon J.
    Li, Mingyao
    Hou, Cuiping
    Yang, Shuzhang
    Glessner, Joseph
    Hakonarson, Hakon
    Bucan, Maja
    Maris, John M.
    Wang, Kai
    [J]. NUCLEIC ACIDS RESEARCH, 2008, 36 (19)
  • [10] Genome-wide association study for milk somatic cell score in holstein cattle using copy number variation as markers
    Duran Aguilar, M.
    Roman Ponce, S. I.
    Ruiz Lopez, F. J.
    Gonzalez Padilla, E.
    Vasquez Pelaez, C. G.
    Bagnato, A.
    Strillacci, M. G.
    [J]. JOURNAL OF ANIMAL BREEDING AND GENETICS, 2017, 134 (01) : 49 - 59